Agree with jmike … convert to NTFS unless you need to stay with FAT32 (ie to dual boot win98).
One problem is that if chkdsk doesn’t complete it’s scan it will start again at the next boot (read the message during the 10 second countdown for example).
This should get rid of it though (provided you don’t have a real hard disk problem)
Run Regedit and navigate to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager. Now double-click on BootExecute. When the dialog box opens, change the value to autocheck autochk * and click on OK. Close Regedit. When you restart, chkdisk will not run.
If you want to make a .reg file to import it instead, just copy the info below and paste it into a text file and rename the extension from .txt to .reg, then double click the file to import into the registry.
Windows Registry Editor Version 5.00